, Volume 179, Issue 3, pp 485–497 | Cite as

Quantitative trait loci analysis of stem strength and related traits in soybean

  • Haifeng Chen
  • Zhihui Shan
  • Aihua Sha
  • Baoduo Wu
  • Zhonglu Yang
  • Shuilian Chen
  • Rong Zhou
  • Xinan Zhou


Stem strength is one of the major influencing factors of lodging in soybean [Glycine max (L.) Merr.] as well as other crops. To identify quantitative trait loci (QTL) associated with stem strength and related traits in soybean, a recombinant inbred line (RIL) population consisting of 165 lines derived from Zhongdou No. 29 × Zhongdou No. 32 was used in 3 years. Significant positive correlations were found among the four traits (stem strength, stem diameter, number of nodes, root dry weight). A linkage map spanning 1,240.7 cM was constructed using 245 SSR (simple sequence repeat) markers and a phenotypic marker (leaflet shape). By composite interval mapping and two-round strategy of QTL meta-analysis, 32 consensus QTL and 19 unique QTL were identified, respectively. Of eight pleiotropic unique QTL, two QTL (uq.A2-2 and uq.A2-3) located at the intervals of 23.2–26.8 and 38.5–42.4 cM on linkage group A2, respectively, were associated with all the four traits. Additive × environment (ae) interaction effects, epistasis (aa) and epistasis × environment (aae) interaction effects of QTL were detected as well. The results provide useful information for further genetic studies on stem strength of soybean.


Soybean Stem strength SSR QTL Meta-analysis 



The study was supported by National Natural Science Foundation (30871554 and 30900906) and the transgenic project (2008ZX08004-005 and 2009ZX08009-133B) from Ministry of Agriculture, People’s Republic of China. The critical reading of the manuscript by Prof. Zaiyun Li (Huazhong Agricultural University, Wuhan), the precise analyzing of the data and the serious revising of the manuscript by Dr Jiaqin Shi in our institute is greatly appreciated. We greatly thank the two anonymous reviewers for critical reading and suggestions on how to improve the manuscript.

Supplementary material

10681_2011_382_MOESM1_ESM.doc (42 kb)
Supplementary material 1 (DOC 41 kb)
10681_2011_382_MOESM2_ESM.doc (68 kb)
Supplementary material 2 (DOC 67 kb)


  1. Adelana BO (1980) Relationship between lodging, morphological characters and yield of tomato cultivars. Sci Hortic 13:143–148CrossRefGoogle Scholar
  2. Allan RE (1986) Agronomic comparisons among wheat lines nearly isogenic for three reduced height genes. Crop Sci 26:707–710CrossRefGoogle Scholar
  3. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20:2324–2326PubMedCrossRefGoogle Scholar
  4. Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83PubMedCrossRefGoogle Scholar
  5. Beeck CP, Wroth J, Cowling WA (2006) Genetic variation in stem strength in field pea (Pisum sativum L.) and its association with compressed stem thickness. Aust J Agric Res 57:193–199CrossRefGoogle Scholar
  6. Beeck CP, Wroth JM, Cowling WA (2008) Additive genetic variance for stem strength in field pea (Pisum sativum). Aust J Agric Res 59:80–85CrossRefGoogle Scholar
  7. Berry PM, Sterling M, Mooney SJ (2006) Development of a model of lodging for barley. J Agron Crop Sci 192:151–158CrossRefGoogle Scholar
  8. Board J (2001) Reduced lodging for soybean in low plant population is related to light quality. Crop Sci 41:379–384CrossRefGoogle Scholar
  9. Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546PubMedCrossRefGoogle Scholar
  10. Breitling R, Li Y, Tesson BM, Fu J, Wu C, Wiltshire T, Gerrits A, Bystrykh LV, de Haan G, Su AI, Jansen RC (2008) Genetical genomics: spotlight on QTL hotspots. PLoS Genet 4(10):e1000232PubMedCrossRefGoogle Scholar
  11. Carter PR, Hudelson KD (1988) Influence of simulated wind lodging on corn growth and grain yield. J Prod Agric 1:295–299Google Scholar
  12. Chardon F, Virlon B, Moreau L, Falque M, Joets J, Decousset L, Murigneux A, Charcosset A (2004) Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome. Genetics 168:2169–2185PubMedCrossRefGoogle Scholar
  13. Chen HF, Ge XH, Du XZ, Zhao ZG, Li ZY (2009) Genetic and histological characterization of a novel recessive genic male sterile line of Brassica napus derived from a cross with Capsella bursa-pastoris. Euphytica 167:31–37CrossRefGoogle Scholar
  14. Cho Y, Njiti VN, Chen X, Triwatayakorn K, Kassem MA, Meksem K, Lightfoot DA, Wood AJ (2002) Quantitative trait loci associated with foliar trigonelline accumulation in Glycine max L. J Biomed Biotechnol 2:151–157PubMedCrossRefGoogle Scholar
  15. Cooper RL (1971) Influence of early lodging on yield of soybean [Glycine max (L.) Merr.]. Agron J 63:449–450CrossRefGoogle Scholar
  16. Dunca J (2008) Mechanical properties of cereal stem. Res Agric Eng 54:91–96Google Scholar
  17. Funatsuki H, Kawaguchi K, Matsuba S, Sato Y, Ishimoto M (2005) Mapping of QTL associated with chilling tolerance during reproductive growth in soybean. Theor Appl Genet 111:851–861PubMedCrossRefGoogle Scholar
  18. Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463–473PubMedGoogle Scholar
  19. Hai L, Guo HJ, Xiao SH, Jiang GL, Zhang XY, Yan CS, Xin ZY, Jia JZ (2005) Quantitative trait loci (QTL) of stem strength and related traits in a doubled-haploid population of wheat (Triticum aestivum L.). Euphytica 141:1–9CrossRefGoogle Scholar
  20. Halpin C, Holt K, Chojecki J, Oliver D, Chabbert B, Monties B, Edwards K, Barakats A, Foxon GA (1998) Brown-midrib maize (bm1): a mutation affecting the cinnamyl alcohol dehydrogenase gene. Plant J 14:545–553PubMedCrossRefGoogle Scholar
  21. Hisano H, Sato S, Isobe S, Sasamoto S, Wada T, Matsuno A, Fujishiro T, Yamada M, Nakayama S, Nakamura Y, Watanabe S, Harada K, Tabata S (2007) Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res 14:271–281PubMedCrossRefGoogle Scholar
  22. Hwang TY, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, Hisano H, Sasamoto S, Sato S, Tabata S, Kono I, Hoshi M, Hanawa M, Yano C, Xia Z, Harada K, Kitamura K, Ishimoto M (2009) High-density integrated linkage map based on SSR markers in soybean. DNA Res 16:213–225PubMedCrossRefGoogle Scholar
  23. Hyten DL, Pantalone VR, Sams CE, Saxton AM, Landau-Ellis D, Stefaniak TR, Schmidt ME (2004) Seed quality QTL in a prominent soybean population. Theor Appl Genet 109:552–561PubMedCrossRefGoogle Scholar
  24. Ishimaru K, Togawa E, Ookawa T, Kashiwagi T, Madoka Y, Hirotsu N (2008) New target for rice lodging resistance and its effect in a typhoon. Planta 227:601–609PubMedCrossRefGoogle Scholar
  25. Islam N, Evans EJ (1994) Influence of lodging and nitrogen rate on the yield and yield attributes of oilseed rape (Brassica napus L.). Theor Appl Genet 88:530–534CrossRefGoogle Scholar
  26. Islam MS, Peng S, Visperas RM, Ereful N, Bhuiya MSU, Julfiquar AW (2007) Lodging-related morphological traits of hybrid rice in a tropical irrigated ecosystem. Field Crops Res 101:240–248CrossRefGoogle Scholar
  27. Jones L, Ennos AR, Turner SR (2001) Cloning and characterization of irregular xylem4 (irx4): a severely lignin-deficient mutant of Arabidopsis. Plant J 26:205–216PubMedCrossRefGoogle Scholar
  28. Kashiwagi T, Ishimaru K (2004) Identification and functional analysis of a locus for improvement of lodging resistance in rice. Plant Physiol 134:676–683PubMedCrossRefGoogle Scholar
  29. Kashiwagi T, Madoka Y, Hirotsu N, Ishimaru K (2006) Locus prl5 improves lodging resistance of rice by delaying senescence and increasing carbohydrate reaccumulation. Plant Physiol Biochem 44:152–157PubMedCrossRefGoogle Scholar
  30. Keim P, Olsen TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newsl 15:147–148Google Scholar
  31. Khush GS (1999) Green revolution: preparing for the 21st century. Genome 42:646–655PubMedCrossRefGoogle Scholar
  32. Lee SH, Bailey MA, Mian MAR, Shipe ER, Ashley DA, Parrot WA, Hussey RS, Boerma HR (1996) Identification of quantitative trait loci for plant height, lodging, and maturity in a soybean population segregating for growth habit. Theor Appl Genet 92:516–523CrossRefGoogle Scholar
  33. Ma QH (2009) The expression of caffeic acid 3-O-methyltransferase in two wheat genotypes differing in lodging resistance. J Exp Bot 60:2763–2771PubMedCrossRefGoogle Scholar
  34. Ma QH (2010) Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat. J Exp Bot. doi: 10.1093/jxb/erq107
  35. Ma QH, Xu Y (2008) Characterization of a caffeic acid 3-O-methyltransferase from wheat and its function in lignin biosynthesis. Biochimie 90:515–524PubMedCrossRefGoogle Scholar
  36. Mancuso N, Caviness CE (1991) Association of selected plant traits with lodging of four determinate soybean cultivars. Crop Sci 31:911–914CrossRefGoogle Scholar
  37. Menchey EK, Aycock MK Jr, McIntosh MS (1993) Morphological characteristics associated with lodging of tobacco. Crop Sci 33:58–62CrossRefGoogle Scholar
  38. Noor RBM, Caviness CE (1980) Influence of induced lodging on pod distribution and seed yield in soybeans. Agron J 72:904–906CrossRefGoogle Scholar
  39. Pinthus MJ (1973) Lodging in wheat, barley, and oats: the phenomenon, its causes, and preventive measures. Adv Agron 25:209–263CrossRefGoogle Scholar
  40. Rae AM, Street NR, Robinson KM, Harris N, Taylor G (2009) Five QTL hotspots for yield in short rotation coppice bioenergy poplar: the poplar biomass loci. BMC Plant Biol 9:23. doi: 10.1186/1471-2229-9-23 PubMedCrossRefGoogle Scholar
  41. Reynolds M, Foulkes MJ, Slafer GA, Berry P, Parry MA, Snape JW, Angus WJ (2009) Raising yield potential in wheat. J Exp Bot 60:1899–1918PubMedCrossRefGoogle Scholar
  42. Salas P, Oyarzo-Llaipen JC, Wang D, Chase K, Mansur L (2006) Genetic mapping of seed shape in three populations of recombinant inbred lines of soybean (Glycine max L. Merr.). Theor Appl Genet 113:1459–1466PubMedCrossRefGoogle Scholar
  43. SAS (1999) SAS/SAT User’s Guide, version 8.0. SAS Institute, CaryGoogle Scholar
  44. Sattler SE, Saathoff AJ, Haas EJ, Palmer NA, Funnell-Harris DL, Sarath G, Pedersen JF (2009) A nonsense mutation in a cinnamyl alcohol dehydrogenase gene is responsible for the sorghum brown midrib6 phenotype. Plant Physiol 150:584–595PubMedCrossRefGoogle Scholar
  45. Setter TL, Laureles EV, Mazaredo AM (1997) Lodging reduces yield of rice by self-shading and reductions in canopy photosynthesis. Field Crops Res 49:95–106CrossRefGoogle Scholar
  46. Shi JQ, Li RY, Qiu D, Jiang CC, Long Y, Morgan C, Bancroft I, Meng JL (2009) Unraveling the complex trait of crop yield with QTL mapping in Brassica napus. Genetics 182:851–861PubMedCrossRefGoogle Scholar
  47. Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128PubMedCrossRefGoogle Scholar
  48. Suzuki M, Fujino K, Nakamoto Y, Ishimoto M, Funatsuki H (2010) Fine mapping and development of DNA markers for the qPDH1 locus associated with pod dehiscence in soybean. Mol Breed 25:407–418CrossRefGoogle Scholar
  49. Taylor NG, Scheible WR, Cutler S, Somerville CR, Turner SR (1999) The irregular xylem3 locus of Arabidopsis encodes a cellulose synthase required for secondary cell wall synthesis. Plant Cell 11:769–779PubMedCrossRefGoogle Scholar
  50. Tobias CM, Chow EK (2005) Structure of the cinnamyl-alcohol dehydrogenase gene family in rice and promoter activity of a member associated with lignification. Planta 220:678–688PubMedCrossRefGoogle Scholar
  51. Udall JA, Quijada PA, Lambert B, Osborn TC (2006) Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm. Theor Appl Genet 113(4):597–609PubMedCrossRefGoogle Scholar
  52. Utomo HS, Linscombe SD (2009) Current patents and future development underlying marker-assisted breeding in major grain crops. Recent Pat DNA Gene Seq 3:53–62PubMedCrossRefGoogle Scholar
  53. Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0 software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  54. Verma V, Worland AJ, Sayers EJ, Fish L, Caligari PDS, Snape JW (2005) Identification and characterization of quantitative trait loci related to lodging resistance and associated traits in bread wheat. Plant Breed 124:234–241CrossRefGoogle Scholar
  55. Vignols F, Rigau J, Torres MA, Capeliades M, Puigdomenech P (1995) The brown midrib3 (bm3) mutation in maize occurs in the gene encoding caffeic acid O-methyltransferase. Plant Cell 7:407–416PubMedCrossRefGoogle Scholar
  56. Woods SJ, Swearingin ML (1977) Influence of simulated early lodging upon soybean seed yield and its components. Agron J 69:239–242CrossRefGoogle Scholar
  57. Wu X, Blake S, Sleper DA, Shannon JG, Cregan P, Nguyen HT (2009) QTL, additive and epistatic effects for SCN resistance in PI 437654. Theor Appl Genet 118:1093–1105PubMedCrossRefGoogle Scholar
  58. Xia Z, Tsubokura Y, Hoshi M, Hanawa M, Yano C, Okamura K, Ahmed TA, Anai T, Watanabe S, Hayashi M, Kawai T, Hossain KG, Masaki H, Asai K, Yamanaka N, Kubo N, Kadowaki KI, Nagamura Y, Yano M, Sasaki T, Harada K (2007) An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using a single F2 population. DNA Res 14:257–269PubMedCrossRefGoogle Scholar
  59. Yang J, Zhu J, Williams RW (2007) Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23:1527–1536PubMedCrossRefGoogle Scholar
  60. Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721–723PubMedCrossRefGoogle Scholar
  61. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  62. Zhang G, Gu C, Wang D (2009) Molecular mapping of soybean aphid resistance genes in PI 567541B. Theor Appl Genet 118:473–482PubMedCrossRefGoogle Scholar
  63. Zhou R, Chen HF, Wang XZ, Zhang XJ, Shan ZH, Wu XJ, Cai SP, Qiu DZ, Zhou XA, Wu JS (2009) QTL analysis of yield, yield components and lodging in soybean. Acta Agric Sin 35:821–830CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Haifeng Chen
    • 1
  • Zhihui Shan
    • 1
  • Aihua Sha
    • 1
  • Baoduo Wu
    • 1
  • Zhonglu Yang
    • 1
  • Shuilian Chen
    • 1
  • Rong Zhou
    • 1
  • Xinan Zhou
    • 1
  1. 1.Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesKey Laboratory of Oil Crop Biology of the Ministry of AgricultureWuhanChina

Personalised recommendations